Structure-Function Linkage Database

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Structure-Function Linkage Database

Patricia C. Babbitt¹, Scott C.H. Pegg¹, Shoshana Brown¹, Sunil Ojha¹, and Thomas E. Ferrin²

¹ Department of Biopharmaceutical Sciences
University of California, San Francisco

² Resource for Biocomputing, Visualization, and Informatics
University of California, San Francisco

The relationship between a given protein's structure and its molecular function can be quite complex, yet recently some of the fundamentals have been elucidated through the study of enzyme superfamilies. The Resource for Biocomputing, Visualization, and Informatics (RBVI) and the Babbitt lab are developing the Structure-Function Linkage Database (SFLD) to leverage this information in a manner which will allow users to predict and engineer enzyme function.
The SFLD is now a web-acessible database hosted by the RBVI. Currently supported are methods allowing users to search the database with a protein sequence, keyword (matching enzyme or reaction name), or with a reaction, substrate, product, or partial reaction as described by a SMILES string. Easy (i.e. single click) methods for users to visualize the multiple sequence alignments and protein structures within the SFLD using Chimera are being developed.
A web interface allowing curators of the SFLD to input and update information has recently be implemented, and is used by all current curators.
A paper describing aspects of the SFLD was presented at the Pacific Symposium for Biocomputing in January 2005, and a more detailed mansucript describing SFLD has been published in Biochemistry.
The SFLD is available to the public at http://sfld.rbvi.ucsf.edu.

References:

Pegg SCH, Brown S, Ojha S, Huang CC, Ferrin TE, Babbitt PC, "Representing structure-function relationships in mechanistically diverse enzyme superfamilies." Pac. Symp. Biocomput. 2005, pp. 358-69.
Pegg, SCH, Brown, SD, Ojha, S, Seffernick, J, Meng, EC, Morris, JH, Chang, PJ, Huang, CC, Ferrin, TE, and Babbitt, PC, " Leveraging Enzyme Structure-Function Relationships for Functional Inference and Experimental Design: The Structure-Function Linkage Database." Biochemistry, 45:8, pp. 2545-2555, 2006